The inherent home of the worldwide reservoir of influenza A viruses is the wild waterfowl population (Hinshaw et al., 1982, In: Beare A S (ed). Basic and Applied Influenza Research, CRC Press, Boca Raton, La., pp. 79-104). Infection in water-based avian species is usually subclinical and confined to the intestinal tract. All subtypes of Type A influenza viruses have been detected in waterfowl, and the viruses are usually very stable genetically in these hosts. Influenza viruses have been shown to sporadically infect a wide variety of other host species, and such infection often results in disease (Webster et al., 1992, Microbiol Rev 56:152-179). Once established in a non-waterfowl species, influenza viruses are much less stable and mutation occurs more frequently (Bean et al., 1992, J Virol 66:1129-38). The viruses have been able to adapt to cause sustained infection in a few other species, most notably humans, pigs, horses and poultry. Characterization of the external proteins, hemagglutinin (HA) and neuraminidase (NA), allows influenza A viruses to be classified into 16 HA and 9 NA subtypes. All subtypes can be found in the waterfowl reservoir, but infection of other species appears to be limited to certain subtypes. Influenza viruses have a segmented genome and concurrent infection of a host with more than one virus can result in production of a new virus with a different constellation of genes that differ from either original virus, a process called reasssortment. Influenza viruses can cross into new host species intact or contribute to the appearance of a new subtype in that species through reassortment (Wright et al., 2001, Orthomyxoviruses. In: Knipe D M, Howley P M (eds). Fields Virology, 4th ed. Lippincott. Williams & Wilkins, Philadelphia, pp. 1533-1579). Either of these two scenarios can result in influenza pandemics within the new host species.
The influenza subtypes that have been able to establish and maintain infections in humans and swine are H1, H3, N1 and N2. Humans also can be infected with H2 influenza viruses, a subtype that has not been identified in swine. H2N2 influenza virus has not circulated in the human population for the past 40 years and is currently detected only in avian species (Liu et al., 2004, Virus Genes 29:81-86, Munster et al., 2007, PLoS Pathog 3:e61, Krauss et al., 2004, Vector Borne Zoonotic Dis 4:177-189). There are two distinct lineages of avian H2 influenza viruses. The Eurasian lineage is genetically more similar to human H2 viruses (Schafer et al., 1993, Virology 194:781-788) than the American lineage. Nevertheless, some H2 viruses isolated from North American shorebirds carry HA of the Eurasian lineage, suggesting interregional transmission of the H2 gene (Makarova et al., 1999, J Gen Virol 80 Pt 12:3167-3171). H2 subtypes are presently circulating in birds, especially migratory birds. A variety of influenza subtypes also have been recovered from domestic poultry, but only two subtypes (H5, H7) have been associated with severe disease. Such infections in poultry are systemic in nature rather than being limited to the intestinal tract.
Three human pandemics have occurred in the last century and all three appear to have been due to infection of humans with a virus of avian origin. The 1918 Spanish “flu” was caused by a virus that crossed into humans “in toto”, while the 1957 Asian “flu” (H2N2) and 1968 Hong Kong “flu” (H3N2) were due to reassortment of an avian source virus with a virus pre-existent in the human population (Kawaoka et al., 1989, J Virol 63:4603-4608). Typically, infection of humans with an avian virus does not readily occur because of differences in cell receptors in the two species. Avian influenza viruses prefer to attach to N-acetylneuraminic acid-α2,3-galactose receptor moieties which are found in abundance in avian intestinal tracts but are few in number in human respiratory tracts. Viruses adapted to humans and swine prefer to attach to N-acetylneuraminic acid-α2,6-galactose receptor moieties which are in abundance in human respiratory tracts (Rogers et al., 1983, Virol 127:361-373). Swine are readily infected with both human and avian viruses because their respiratory tracts have an abundance of both receptors. Experimentally, swine have been found to be susceptible to infection with nearly all subtypes (Hinshaw et al., 1981, Infect Immun 34:354-361, Kida et al., 1994, J Gen Virol 75:2183-2188). New reassortant viruses have been recovered from swine experimentally infected with two different influenza viruses at the same time (Webster et al., 1973, Virol 51:149-162). Results of these studies and others resulted in the concept of swine as “mixing vessels” and the concern that swine may contribute to formation of pandemic viruses (Scholtissek, 1990, Med Principles Pract 2:65-71). The close association of humans, swine, ducks and poultry under agricultural conditions in Asia is thought to contribute to the tendency of new pandemics to arise from that part of the world.
Since 1997, influenza viruses in Asia have been a prominent concern in world news (Shortridge et al. 1998, Virol 20:331-342, Shortridge et al., 2000, Vet Microbiol 74:141-147, Lipatov, et al., 2004, J Virol 78: 8951-8959, Webster et al., 2005, Arch Virol Suppl 19:I 17-129). The appearance and uncontrolled spread of a H5N1 influenza virus and the apparent ability of the virus to infect humans with lethal consequences have raised concerns that this virus is a harbinger of the next worldwide influenza pandemic. The H5N1 virus also has characteristics unusual for influenza viruses in its ability to cause fatal infection in waterfowl, the usually subclinical reservoir for influenza viruses (Sturn-Ramirez et al., 2005, J Virol 17:11269-79), and to infect species usually not considered susceptible to influenza virus infection, i.e. felines (Kuiken et al., 2004, Science 306 (5694): 241). The virus is a reassortant of viruses that were circulating in several avian populations: geese, poultry and quail (Webster et al., 2006, Emerg Infect Dis 12:3-8). The H5N1 virus does not currently have the ability to spread readily between humans, but the possibility remains that through mutation or additional reassortment, the virus may acquire that contagious property. To date, infection of swine with the H5N1 influenza virus, while reported in southeast Asia, does not appear to occur frequently (Choi et al., 2005, J Virol 79:10821-5). However, infection of swine with this virus, even if it only occurs rarely, might result in genetic mutations that change its inherent characteristics or could contribute to reassortment that would give rise to a virus with pandemic potential.
Natural infection of swine with avian influenza viruses has been documented worldwide, either as intact viruses or as reassortment events. In the late 1970s, an avian H1N1 virus became widespread in swine populations in Europe and the United Kingdom, displacing the classic swine H1N1 virus that had been imported to that part of the world from the United States (Pensaert et al., 1981, Bull World Health Org 59:75-78). Multiple lineages of H1N1 virus were detected in swine in China in 1993 (Guan et al., 1996, J Virol 70:8041-8046). Some H3N2 viruses recovered from swine in Asia since the 1970s appear to be entirely of avian origin (Kida et al., 1988, Virol 162:160-166). More frequently, avian viruses contribute genes to new reassortant viruses found in swine. In 1993, influenza viruses that were reassortants of avian and human viruses were recovered from pigs in Italy (Castrucci et al., 1993, Virol 193:503-506). Since 1998, swine in the United States have been infected with triple reassortant viruses with NP, M and NS genes from the classic H1N1 swine virus; HA, NA and PB1 genes from human viruses; and PA and PB2 polymerase genes derived from an avian virus (Zhou et al., 1999, J Virol 73:8851-8856, Webby et al., 2000, J Virol 74:8243-8251, Webby et al., 2004, Virus Res 103:67-73). The mixed-source internal genes in this triple reassortant appear to have contributed to a virus that replicates efficiently in swine but is able to “mix and match” the genes for the external HA and NA proteins quite readily. Some studies have implicated avian polymerase genes in enabling influenza viruses to cross species boundaries and establish in new hosts (Kawaoka et al., 1989, J Virol 63:4603-4608, Gabriel et al., 2005, Proc Natl Acad Sci USA 102(51):18590-5). Although early studies indicated that avian influenza viruses of most subtypes could infect pigs, a pilot study with an H5N1 virus isolated from birds in Vietnam in 2004 revealed only mild infection and no spread of virus to contact pigs. A serologic study of 3175 pigs from the regions in Asia in which the H5N1 influenza virus was responsible for widespread death loss in poultry revealed only 8 (0.25%) sera with antibodies against the virus (Choi et al., 2005, J Virol 79:10821-5). An assessment of the ability of these viruses to infect swine and evaluation of the genetic changes that occur during such infection would provide information on the degree of risk that swine could contribute to the establishment of a new pandemic virus.